Search found 350 matches

by SaxsMax
2008.04.24 10:09
Forum: Ab Initio Shape Determination
Topic: Enantiomorphic differences between DAMMIN and BUNCH models
Replies: 1
Views: 3443

It is quite normal to obtain enanthiomorhs in Dammin as they have absolutely
the same scattering. The program supcomb can superimpose the models
by taking into account possible enanthiomorhs.
Use Bunch model as a reference and Dammin one as a structure to superimpose.
by SaxsMax
2008.04.24 10:03
Forum: Ab Initio Shape Determination
Topic: Multiple Gasbor Runs Same Output pdb
Replies: 3
Views: 5397

One question remains - is this good enough or would it be better to give truly random numbers like nanoseconds ? Yes, this is enough. /lo logfile /sy particle symmetry /id project description /sd random seed /mo molecular shape ?? /h help This is a complete list. If you need to input more details, ...
by SaxsMax
2008.04.24 09:54
Forum: Ab Initio Shape Determination
Topic: More residues in GASBOR ?
Replies: 1
Views: 4680

1. The complaint should be actually Number of residues+waters exceeds 8000 The program reduces the number of dummy waters and continue. 2. In fact Gasbor should not be used for proteins bigger than ~1000 AA Dammin is much better for such proteins. We put a limit of 8000 for those who desperately wan...
by SaxsMax
2008.03.25 21:17
Forum: Working with Models
Topic: fitting the experimental intensities in Crysol 2.5
Replies: 1
Views: 3779

At least in Crysol26 the intensities should be the same
in both cases.
by SaxsMax
2008.03.25 21:12
Forum: Working with Models
Topic: question for CRYSOL 2.5
Replies: 2
Views: 4467

Dro of 0.075 e/A3 is indeed a bit too much and kept for special cases. Normally, it should not exceed 0.05. On the other hand, please notice that for small proteins (like lysozyme) the contribution of the shell is more significant compared to larger particles as atomic and excluded volume scattering...
by SaxsMax
2008.03.25 20:58
Forum: Working with Models
Topic: CRYSOL paper: About Correct formulas for (12) and (13)
Replies: 1
Views: 4063

"Correction 1" is correct as d=s/2PI
by SaxsMax
2008.03.20 21:26
Forum: Ab Initio Shape Determination
Topic: Gasbor and double helix
Replies: 2
Views: 3852

Unfortunately there is no helical symmetry in Gasbor.
by SaxsMax
2008.03.20 21:24
Forum: Ab Initio Shape Determination
Topic: Program for make many run automatically with gasbor
Replies: 3
Views: 4371

As gasbor can be done in a batch mode
(for help type e.g. "gasbor22i.exe /h")
you can simply create a bat file containing
multiple Gasbor calls
by SaxsMax
2008.03.20 21:15
Forum: Working with Models
Topic: Option for explicit hydrogens (CRYSOL)
Replies: 1
Views: 4479

Normally, all hydrogens are ignored by Crysol while reading PDB file and then simulated according to the atomic group. "Account for explicit hydrogens" option gives the possibility to read all hydrogens from the PDB file. In this case Crysol will not add any further hydrogens and all the atoms are h...
by SaxsMax
2008.03.20 21:09
Forum: Working with Models
Topic: Ra and Vol after parameter fitting (CRYSOL logfile)
Replies: 3
Views: 5694

Hydra is hydration which is computes as following

Mh2o (Border volume)*(Solvent density+Border contrast)
---- * -----------------------------------------------
Eh2o Molecular mass of the macromolecule

where Mh2o = 18 dalton, Eh2o = 10 electrons
by SaxsMax
2008.03.20 21:05
Forum: Working with Models
Topic: Ra and Vol after parameter fitting (CRYSOL logfile)
Replies: 3
Views: 5694

Indeed, by the prediction of the scattering without fitting the data (i.e. with the default parameters) V=N*4/3*PI*ra^3 However in case of fitting the experimental data the ra and volume parameters are decoupled and the above equation is not kept in the adjustment of ra and vol minimizing the discre...
by SaxsMax
2008.03.06 14:13
Forum: Rigid Body Modelling
Topic: what is the principle in transformation subunit of MASSHA?
Replies: 1
Views: 3633

Massha does the local refinement of the models,
so that it is better to have a rough idea how the subunits are
arranged. If you need to do a global search it is better to use SASREF instead.

Ideally, chi should be close to 1.0
by SaxsMax
2008.03.06 14:08
Forum: Ab Initio Shape Determination
Topic: Gasbor22iqw and Gasbor22pqw
Replies: 1
Views: 3189

i stands for intensity, i.e. this is the reciprocal space version fitting the
experimental scattering data.
p stand for p(r), i.e. this is a real space version which fits distance distribution function computed from the SAXS curve
by SaxsMax
2008.03.06 14:06
Forum: Ab Initio Shape Determination
Topic: DAMMIN GASBOR AND RNA molecules
Replies: 1
Views: 3409

Probably nothing has to be adjusted in DAMMIN.
On contrary, GASBOR is only applicable for proteins
and it is better to avoid using it for nucleic acids.
by SaxsMax
2008.03.06 14:04
Forum: Ab Initio Shape Determination
Topic: Gasbor and high NSD values
Replies: 2
Views: 4776

In general, it is normal that GASBOR models
yield higher NSD values compared to DAMMIN ones.
However, NSD of 2.8- 3.2 is a bit too much. Do the superposed
GASBOR models look the same by eye?